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    Helena Rasche
    @hexylena:matrix.org
    [m]
    soudns like you
    gmauro
    @gmauro:matrix.org
    [m]
    I have this warning in the 21.09 log:
    /opt/galaxy/server/lib/galaxy/jobs/handler.py:360: SAWarning: Coercing Subquery object into a select() for use in IN(); please pass a select() construct explicitly
    any ideas what is?
    1 reply
    slugger70
    @slugger70:matrix.org
    [m]
    Sorry mate, I've never seen it.
    gmauro
    @gmauro:matrix.org
    [m]
    but you didn't migrate yet, no? :)
    slugger70
    @slugger70:matrix.org
    [m]
    yeah we did last week
    gmauro
    @gmauro:matrix.org
    [m]
    ah, super!
    Helena Rasche
    @hexylena:matrix.org
    [m]
    file a bug for the devs to track down I'd sya
    slugger70
    @slugger70:matrix.org
    [m]
    does it effect anything?
    i.e. Is everything still working?
    gmauro
    @gmauro:matrix.org
    [m]
    still looking if everything is ok
    but at least gx processes are running
    slugger70
    @slugger70:matrix.org
    [m]
    cool.
    Helena Rasche
    @hexylena:matrix.org
    [m]
    SAwarnings feel pretty common
    cat-bro
    @cat-bro:matrix.org
    [m]
    I've seen that. I assumed it was a result of changing sqlalchemy version
    Marius
    @mvdbeek:matrix.org
    [m]
    It is, nothing to worry about. In some flavor or another these have always been there. This one we need to address before moving the sqlalchemy 2.0. I think we can turn these warnings off in releases
    I am surprised to see how the installation of postgresql could be that "easy". But, I am stuck in some error in the step that follows the DB setup.
    The error message is too long: the first part is:
    TASK [galaxyproject.galaxy : Install Galaxy base dependencies]

    The last part was like this: WARNING: Discarding https://wheels.galaxyproject.org/simple/futures/futures-3.1.1.tar.gz (from https://wheels.galaxyproject.org/simple/futures/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.\nERROR: Could not find a version that satisfies the requirement futures==3.1.1 (from versions: 0.2.python3, 0.1, 0.2, 1.0, 2.0, 2.1, 2.1.1, 2.1.2, 2.1.3, 2.1.4, 2.1.5, 2.1.6, 2.2.0, 3.0.0, 3.0.1, 3.0.2, 3.0.3, 3.0.4, 3.0.5, 3.1.0, 3.1.1)\nERROR: No matching distribution found for futures==3.1.1\n"}

    PLAY RECAP **
    vm : ok=53 changed=0 unreachable=0 failed=1 skipped=33 rescued=0 ignored=0

    Sang Chul Choi
    @goshng
    Sorry for the long error message. My question is not to get help about the error that I got. I would appreciate it though. I was wondering where I should ask that kind of question above.
    I have tried to reread the tutorial above to see if there is any point that I could follow.
    But, I do not know where I should ask. First, I have been working in the field of evolutionary sequence analysis. I am working with a student to setup a galaxy instance using Ansible. I will appreciate your help. I am new to galaxy admin although I was a galaxy user for a long time. Thank you.
    Marius
    @mvdbeek:matrix.org
    [m]
    Ah, that version of futures has been yanked from pypi
    Which version of Galaxy are you trying to install ?
    Nicola Soranzo
    @nsoranzo:matrix.org
    [m]
    futures has never been a requirement for Galaxy, as far as I can tell
    Marius
    @mvdbeek:matrix.org
    [m]
    I think the oldest release that required futures 3.1.1 was 20.09, which is not supported anymore
    @goshng: If you switch out galaxy_commit_id to something newer, like release_21.09 this should work
    Nicola Soranzo
    @nsoranzo:matrix.org
    [m]
    Ah, git log -p --follow -- lib/galaxy/dependencies/pinned-requirements.txt lied to me!
    Marius
    @mvdbeek:matrix.org
    [m]
    yeah, the history was interrupted when we moved to poetry
    Nicola Soranzo
    @nsoranzo:matrix.org
    [m]
    It decided to follow the wrong file
    Helena Rasche
    @hexylena:matrix.org
    [m]
    huh, I didn't know about --follow, I wish I'd known that one earlier.
    Nicola Soranzo
    @nsoranzo:matrix.org
    [m]
    I use it all the time, it should be the default
    Helena Rasche
    @hexylena:matrix.org
    [m]
    testing out mamba instead of conda for one galaxy deployment I'm responsible for and wow it's faster
    fingers crossed nothing goes wrong
    Marius
    @mvdbeek:matrix.org
    [m]
    Is it much faster than adding --strict-channel-priority to the conda create flags ?
    We have this in the backlog ... galaxyproject/galaxy#12788
    Helena Rasche
    @hexylena:matrix.org
    [m]
    would be nice to benchmark
    currently I don't have an answer for that
    Marius
    @mvdbeek:matrix.org
    [m]
    I guess it really depends ... but since bioconda is recommending that we should just get around and do it
    Helena Rasche
    @hexylena:matrix.org
    [m]
    i'll run a n=1 test for ya
    mamba: 10s
    conda: 2min
    conda-strict: 42s
    # Mamba
    (base) galaxy@bioinf-galactus:/srv/galaxy/var/dependencies/_conda$ time /srv/galaxy/var/dependencies/_conda/bin/mamba create -y --quiet --override-channels --channel conda-forge --channel bioconda --channel defaults hisat2=2.2.1 samtools=1.12 seqtk=1.3 --name test-mamba
    ...
    real    0m9.918s
    user    0m8.605s
    sys     0m0.846s
    
    # Conda (default)
    (base) galaxy@bioinf-galactus:/srv/galaxy/var/dependencies/_conda$ time /srv/galaxy/var/dependencies/_conda/bin/conda create -y --quiet --override-channels --channel conda-forge --channel bioconda --channel defaults hisat2=2.2.1 samtools=1.12 seqtk=1.3 --name test-conda
    # The first bit is VERY slow
    Collecting package metadata (current_repodata.json): ...working... done
    Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
    Collecting package metadata (repodata.json): ...working... done
    Solving environment: ...working...
    ...
    real    1m59.373s
    user    1m45.825s
    sys     0m4.085s
    
    
    # Conda (--strict-channel-priority)
    
    (base) galaxy@bioinf-galactus:/srv/galaxy/var/dependencies/_conda$ time /srv/galaxy/var/dependencies/_conda/bin/conda create -y --quiet --override-channels --channel conda-forge --channel bioconda --channel defaults hisat2=2.2.1 samtools=1.12 seqtk=1.3 --name test-conda-strict --strict-channel-priority
    # The first bit fails much faster.
    Collecting package metadata (current_repodata.json): ...working... done
    Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
    Collecting package metadata (repodata.json): ...working...
    ...
    real    0m42.747s
    user    0m31.254s
    sys     0m2.513s
    some notes inline in the snippet. anyway I'm out for the weekend.
    Marius
    @mvdbeek:matrix.org
    [m]
    Enjoy!
    Nicola Soranzo
    @nsoranzo:matrix.org
    [m]
    Also from my experience mamba is much faster than conda (and I've had the channel priority strict turned on since a while ago), and it resolves complex sets of requirements that conda fails to.
    Sang Chul Choi
    @goshng
    @mvdbeek:matrix.org Thank you! The change to galaxy_commit_id passed the step.
    Marius
    @mvdbeek:matrix.org
    [m]
    That's already on dev, do we need to backport this ?
    It's just a warning, so I thought that won't be necessary
    Nate Coraor
    @natefoo:matrix.org
    [m]
    No, definitely not necessary to backport, I didn't know it was on dev.